Hi all, I have just got dual monitors up and running for my system.
I have managed to get the taskbar on the monitor I want it to be, but the system seems a bit confused about which it the primar monitor.
When I open new windows, they open in the window which doesn't have the taskbar. it's also where the stystem likes to put the computer and home icons.
I've checked the config file, and they system seems to have the correct monitor set as the primary monitor.

On further fiddleing, it seems that the problem only manifests when the primary monitor is the right hand monitor. If I go and swap the monitors in settings, it doesn't open windows on the wrong screen - but of course this is no solution because the monitors aren't actually in that order on my desk (and I can't sawp them because they are different sizes and it just works better this way).

If I swap the hardware cables and try again, I get the same result. It just can't handle having the right hand monitor as the primary.

Also, I have found that the problem is not for all apps.
Apps which open on the right monitor :
- emacs
- hedgewars
- mendeley
- libre office writer
- vlc
- amarok
- chromium

Linux Mint 13 x64, MATE, AMD Radeon video card with proprietary drivers. Got exactly the same problem. I also have primary big monitor on the right and most of the windows appear on the left one. While the small one was on the right everything was fine, but I had to swap them...

Setting primary monitor in .config/monitors.xml doesn't help as doesn't help identical setting in "Monitors" section in Control Center.

Had this problem, too, on Maya 32-bit with MATE. Using a NVIDIA 610M on an HP 9910us. But instead of dual monitors, I was running a projector. Didn't have the time to test it out to the extent you two did, but it was annoying having taskbar and desktop icons on the projector's screen, open up a presentation in Libre Office that showed on the laptop, but then the actual presentation show on the projector. Could only seem to get something usable whenever I mirrored the screens. But sorta defeats the purpose of dual-screens/projector usage, doesn't it?

THANK YOU! I have suffered this problem since i started to use Linux mint cinnamon and even sometimes when i used ubuntu. Its been driving me mad for ages. The Monitors.xml trick fixed what I thought was a Nvidia-settings problem for ages, I had to change the settings every time I booted the PC, in 2 minuets you folk saved my sanity.

Sorry to bump this old thread, but this is one of the highest ranked results in Google when searching for this problem.

I have the same problem as OP, when I open new windows in both Chromium and Firefox, they open on my left monitor, although I've set my right monitor as the primary monitor.

I'm on a pretty empty Mint 15 installation, using MATE 1.6.0.

Opening terminals and Caja works as I want (actually, they both open new windows on the monitor where my current window is), but Firefox and Chromium always open new windows on the left monitor.

I've set the right monitor as the primary one in ~/.config/monitors.xml, and I've also checked "Make this the primary display for the X screen" in NVIDIA X Server Settings, and set the right monitor in xrandr as primary using "xrandr --output <output> --primary". New browser windows still show up on the wrong screen, and the login screen also shows up on the wrong screen.

I think I found a much simpler solution. Let me preface this by saying that I did make the changes to the monitors.xml file mentioned above, and didn't have success upon reboot.

However, I found that if you disable one monitor--and of course have "Miror Displays" unchecked" that the enabled monitor automatically becomes the "primary", the monitor with all the menues. Then when you reenable the other monitor the monitor that was most recently the primary stays primary.

So, if I want my laptopt to be primary, I simply turn off my attached VGA display in the Display Settings GUI. Then the laptop becomes primary and stays primary when I reenable the second display--and vice versa. It beats editing the .xml file and logging out, for sure.